SN 2011dh: DISCOVERY OF A TYPE IIb SUPERNOVA FROM A COMPACT PROGENITOR IN THE NEARBY GALAXY M51

On 2011 May 31 UT a supernova (SN) exploded in the nearby galaxy M51 (the Whirlpool Galaxy). We discovered this event using small telescopes equipped with CCD cameras and also detected it with the Palomar Transient Factory survey, rapidly confirming it to be a Type II SN. Here, we present multi-color ultraviolet through infrared photometry which is used to calculate the bolometric luminosity and a series of spectra. Our early-time observations indicate that SN 2011dh resulted from the explosion of a relatively compact progenitor star. Rapid shock-breakout cooling leads to relatively low temperatures in early-time spectra, compared to explosions of red supergiant stars, as well as a rapid early light curve decline. Optical spectra of SN 2011dh are dominated by H lines out to day 10 after explosion, after which He I lines develop. This SN is likely a member of the cIIb (compact IIb) class, with progenitor radius larger than that of SN 2008ax and smaller than the eIIb (extended IIb) SN 1993J progenitor. Our data imply that the object identified in pre-explosion Hubble Space Telescope images at the SN location is possibly a companion to the progenitor or a blended source, and not the progenitor star itself, as its radius (~1013 cm) would be highly inconsistent with constraints from our post-explosion spectra.

SNP discovery using Next Generation Transcriptomic Sequencing in Atlantic herring (Clupea harengus)

The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximise cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population genomic studies in the wild.

Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake

The growing accessibility to genomic resources using next-generation sequencing (NGS) technologies has revolutionized the application of molecular genetic tools to ecology and evolutionary studies in non-model organisms. Here we present the case study of the European hake (Merluccius merluccius), one of the most important demersal resources of European fisheries. Two sequencing platforms, the Roche 454 FLX (454) and the Illumina Genome Analyzer (GAII), were used for Single Nucleotide Polymorphisms (SNPs) discovery in the hake muscle transcriptome. De novo transcriptome assembly into unique contigs, annotation, and in silico SNP detection were carried out in parallel for 454 and GAII sequence data. High-throughput genotyping using the Illumina GoldenGate assay was performed for validating 1,536 putative SNPs. Validation results were analysed to compare the performances of 454 and GAII methods and to evaluate the role of several variables (e.g. sequencing depth, intron-exon structure, sequence quality and annotation). Despite well-known differences in sequence length and throughput, the two approaches showed similar assay conversion rates (approximately 43%) and percentages of polymorphic loci (67.5% and 63.3% for GAII and 454, respectively). Both NGS platforms therefore demonstrated to be suitable for large scale identification of SNPs in transcribed regions of non-model species, although the lack of a reference genome profoundly affects the genotyping success rate. The overall efficiency, however, can be improved using strict quality and filtering criteria for SNP selection (sequence quality, intron-exon structure, target region score).

Improving Recall of Regular Expressions for Information Extraction

Learning or writing regular expressions to identify instances of a specific
concept within text documents with a high precision and recall is challenging.
It is relatively easy to improve the precision of an initial regular expression
by identifying false positives covered and tweaking the expression to avoid the
false positives. However, modifying the expression to improve recall is difficult
since false negatives can only be identified by manually analyzing all documents,
in the absence of any tools to identify the missing instances. We focus on partially
automating the discovery of missing instances by soliciting minimal user
feedback. We present a technique to identify good generalizations of a regular
expression that have improved recall while retaining high precision. We empirically
demonstrate the effectiveness of the proposed technique as compared to
existing methods and show results for a variety of tasks such as identification of
dates, phone numbers, product names, and course numbers on real world datasets

Moytirra:Discovery of the first known deep-sea hydrothermal vent field on the slow-spreading Mid-Atlantic Ridge north of the Azores

Geological, biological, morphological, and hydrochemical data are presented for the newly discovered Moytirra vent field at 45^oN. This is the only high temperature hydrothermal vent known between the Azores and Iceland, in the North Atlantic and is located on a slow to ultraslow-spreading mid-ocean ridge uniquely situated on the 300 m high fault scarp of the eastern axial wall, 3.5 km from the axial volcanic ridge crest. Furthermore, the Moytirra vent field is, unusually for tectonically controlled hydrothermal vents systems, basalt hosted and perched midway up on the median valley wall and presumably heated by an off-axis magma chamber. The Moytirra vent field consists of an alignment of four sites of venting, three actively emitting "black smoke," producing a complex of chimneys and beehive diffusers. The largest chimney is 18 m tall and vigorously venting. The vent fauna described here are the only ones documented for the North Atlantic (Azores to Reykjanes Ridge) and significantly expands our knowledge of North Atlantic biodiversity. The surfaces of the vent chimneys are occupied by aggregations of gastropods (Peltospira sp.) and populations of alvinocaridid shrimp (Mirocaris sp. with Rimicaris sp. also present). Other fauna present include bythograeid crabs (Segonzacia sp.) and zoarcid fish (Pachycara sp.), but bathymodiolin mussels and actinostolid anemones were not observed in the vent field. The discovery of the Moytirra vent field therefore expands the known latitudinal distributions of several vent-endemic genera in the north Atlantic, and reveals faunal affinities with vents south of the Azores rather than north of Iceland. © 2013. American Geophysical Union. All Rights Reserved.

All the World's a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health

The recent explosion of genetic and clinical data generated from tumor genome analysis presents an unparalleled opportunity to enhance our understanding of cancer, but this opportunity is compromised by the reluctance of many in the scientific community to share datasets and the lack of interoperability between different data platforms. The Global Alliance for Genomics and Health is addressing these barriers and challenges through a cooperative framework that encourages "team science" and responsible data sharing, complemented by the development of a series of application program interfaces that link different data platforms, thus breaking down traditional silos and liberating the data to enable new discoveries and ultimately benefit patients.

X-ray driven evaporation of exoplanet atmospheres: discovery of a uniquely suited test system

The evaporation of exoplanetary atmospheres is thought to be driven by high-energy irradiation. However, the actual mass loss rates are not well constrained. Co-I Kipping has recently discovered that the star KOI-314, an M1V dwarf at 65 pc distance, is orbited by two earth-sized planets, the inner one of them rocky and the outer one gaseous (P_orb = 14d and 23d). Other recent works have shown an abundance of small rocky planets in very close orbits around their host stars, suggesting that the stellar high-energy irradiation evaporates away gaseous envelopes. KOI-314 is the first nearby system in which earth-sized planets of both types are detected, allowing us to constrain the efficiency of planetary evaporation if the stellar X-ray irradiation is measured. We therefore propose a 10 ks Chandra ACIS-S pointing to determine the stellar X-ray luminosity and hardness ratio. The accuracy of the orbital solution decreases quickly due to Transit-Timing Variations, which is why we ask for DDT.

Phenotype-Based Discovery of 2-[(E)-2-(Quinolin-2-yl)vinyl]phenol as a Novel Regulator of Ocular Angiogenesis

Retinal angiogenesis is tightly regulated to meet oxygenation and nutritional requirements. In diseases such as proliferative diabetic retinopathy and neovascular age-related macular degeneration, uncontrolled angiogenesis can lead to blindness. Our goal is to better understand the molecular processes controlling retinal angiogenesis and discover novel drugs that inhibit retinal neovascularization. Phenotype-based chemical screens were performed using the ChemBridge Diverset^TM library and inhibition of hyaloid vessel angiogenesis in Tg(fli1:EGFP) zebrafish. 2-[(E)-2-(Quinolin-2-yl)vinyl]phenol, (quininib) robustly inhibits developmental angiogenesis at 4–10 μM in zebrafish and significantly inhibits angiogenic tubule formation in HMEC-1 cells, angiogenic sprouting in aortic ring explants, and retinal revascularization in oxygen-induced retinopathy mice. Quininib is well tolerated in zebrafish, human cell lines, and murine eyes. Profiling screens of 153 angiogenic and inflammatory targets revealed that quininib does not directly target VEGF receptors but antagonizes cysteinyl leukotriene receptors 1 and 2 (CysLT_1–2) at micromolar IC₅₀ values. In summary, quininib is a novel anti-angiogenic small-molecule CysLT receptor antagonist. Quininib inhibits angiogenesis in a range of cell and tissue systems, revealing novel physiological roles for CysLT signaling. Quininib has potential as a novel therapeutic agent to treat ocular neovascular pathologies and may complement current anti-VEGF biological agents.

Women of Letters: Gender, Writing and the Life of the Mind in Early Modern England

Women of letters writes a new history of English women's intellectual worlds using their private letters as evidence of hidden networks of creative exchange. The book argues that many women of this period engaged with a life of the mind and demonstrates the dynamic role letter-writing played in the development of ideas. Until now, it has been assumed that women's intellectual opportunities were curtailed by their confinement in the home. This book illuminates the household as a vibrant site of intellectual thought and expression. Amidst the catalogue of day-to-day news in women's letters are sections dedicated to the discussion of books, plays and ideas. Through these personal epistles, Women of letters offers a fresh interpretation of intellectual life in the late seventeenth and early eighteenth centuries, one that champions the ephemeral and the fleeting in order to rediscover women's lives and minds.

Conto de fadas: o imaginário na aprendizagem da lectoescrita

Esta investigação, cujo estudo empírico se desenvolveu através de um projecto de investigação-acção, numa turma do 1º ano de escolaridade, da Escola dos Combatentes em Ovar, no ano lectivo de 2008/2009 e cuja professora é, simultaneamente, a investigadora, parte do pressuposto de que a descoberta e compreensão da natureza, função e funcionamento do nosso sistema de escrita faz uso de processos racionais mas não dispensa a intervenção de processos afectivos que se inscrevem na área do imaginário e tenta compreender de que forma a exploração do conto de fadas em sala de aula associada à utilização de técnicas do método global pode influenciar a aprendizagem da leitura e da escrita na referida turma. O estudo tem como objectivos reabilitar o imaginário no âmbito da Educação e enfrentar os índices de insucesso escolar no que se refere à aprendizagem da leitura e da escrita nos dois primeiros anos de escolaridade. Inicia-se esta tese com uma abordagem às questões teóricas que norteiam a investigação, nomeadamente, no que se refere ao imaginário, ao conto de fadas e à aprendizagem da leitura e da escrita. Os resultados indicam que à excepção de uma criança que apresentava problemas de natureza cognitiva, o sucesso académico das crianças desta turma foi de 100% quer no final do 1º ano quer no final do 2º ano de escolaridade. De todas as crianças da turma, 79,1% atingiram, no final do 1º ano, um nível de proficiência na leitura e na escrita semelhante ao que é expectável para o final do 2º ano de escolaridade.

Feminist Genealogies in the Writing of the Self

Maria Tamboukou links Foucauldian ideas to feminism and education. Its central argument is that the Foucauldian notion of 'technologies of the self' needs to be gendered and contextualized. This argument is pursued through a genealogical analysis of auto/biographical narratives of women educators at the turn of the nineteenth century. This is a new theoretical approach, since Foucault's work has proved to be of great interest to feminist scholars, but as yet, his theroies have only intermittently been used in educational feminist work. The genealogical analysis of situated female sujectivities has highlighted the importance of space in the 'technologies of the female self' and has reconsidered the private/public couplet. It has acted as a continuous source of uncertainty, experimenting with Foucauldian questions of what we are, of how we have become what we are, but also and perhaps most importantly of how we can become other than what we are already.

‘Not like rose-tinted glasses… like taking a pair of dirty glasses off’: A pilot intervention using positive emotions in expressive writing

Studies conducted in various contexts and with varied populations have found expressive writing enhances physical and psychological wellbeing. This pilot intervention study countered the predominantly quantitative evidence by adopting a qualitative methodology, exploring the experience of using positive emotions in expressive writing. Participants (n = 10), who all had previous experience in expressive writing, were asked to select one of ten positive emotion cards (PECs) each day for three days. Participants were then asked to write expressively through the ‘lens’ of their chosen emotion. Semi-structured interviews were conducted and experiences were evaluated using Thematic Analysis. The results identified two main themes that compared the experience of expressive writing both with and without the PECs. The first theme, Processing (without the PECs) contained three sub-themes: sense of relief, habitual perspective and reactive to experience. The second main theme, Progressing (with the PECs) contained three different sub-themes: sense of direction, changed perspective and interactive with experience. This study found that, for expressive writers, positive emotions may function in three ways: to relate to others or self-expand, to move past challenges cognitively or change unconstructive perspectives, and finally as a way to interactively link or ‘bridge’ from the written subject matter to constructive action, thus breaking cycles of reactive writing and rumination. Implications of the study on the practice of expressive writing and its potential as a positive psychology intervention (PPI) are discussed.